Water quality in lakes is influenced by a large number of watershed and lake characteristics. In this study, we examined the relative effects of watershed land use and lake morphology on the trophic state of 19 lakes in the Yunnan plateau and lower Yangtze floodplain, the two most eutrophic regions in China. Trophic state parameters consisted of total nitrogen, total phosphorus, chemical oxygen demand, chlorophyll-a, Secchi depth, and trophic state index, while lake morphometric variables included area, maximum depth, mean depth, water residence time (WRT), volume, and length to width ratio. Percentages of forest, grassland, cropland, unused land, built-up land, and water body in each lake's watershed were extracted from a land use map interpreted from Landsat TM images. A t-test indicated that lower Yangtze floodplain lakes were shallower and had higher percentages of cropland and built-up land in watersheds than Yunnan plateau lakes. Pearson's correlation analysis indicated that both watershed land use and lake morphometric variables were significantly related to most of the trophic state parameters. However, stepwise regression analyses demonstrated that the trophic state of the lower Yangtze floodplain lakes was mainly controlled by the percentages of cropland and built-up land in watersheds, while that of Yunnan plateau lakes was mostly determined by the lake depth and WRT. These results suggest that the relative effects of watershed land use and lake morphology on lake trophic state are dependent on the lake's location. This study can provide some useful information in watershed land use management for controlling eutrophication in Chinese lakes.